The North Mokelumne River on the left and Tyler Island on the right. A new study says that past management of the delta was completely wrong and now are going to turn around there thinking. Tyler Island in the San Joaquin delta is more than twenty feet below sea level and is basically a giant hole in the ground surrounded by levees. TUESDAY, FEBRUARY 06, 2007 KURT ROGERS/THE CHRONICLE SACRAMENTO THE CHRONICLE
SFC DELTA_0027_kr.jpg MANDATORY CREDIT FOR PHOTOG AND SF CHRONICLE / -MAGS OUT

The Sacramento-San Joaquin River Delta faces economic and environmental collapse, but fortifying its weak levees isn't the answer, according to a report released Wednesday.

The provocative report by the Public Policy Institute of California calls for radically changing how the delta has been managed for the last 70 years. Instead of maintaining it as a freshwater body, the institute suggests turning it back into an estuary that fluctuates between fresh and salty conditions.

The report's authors say it's not possible to preserve the delta's status quo. Ultimately, they say, levees will collapse wholesale regardless of continuing and expensive efforts to bolster them.

The best solution could involve building a canal to move freshwater through the region and into the giant Tracy-area pumps that send water to Southern California, the report concludes. A similar plan to build a peripheral canal was bitterly contested until voters, largely in Northern California, killed the plan in 1982.

In spite of its controversial conclusions, the report by the nonpartisan policy-research organization has spurred interest in Sacramento. Hours after its release, Gov. Arnold Schwarzenegger announced appointees to a delta task force that will study the report's findings and recommend a new way to manage the delta.

And as another example of the delta's deteriorating environment, a coalition of environmental groups asked Wednesday that the delta smelt -- a small fish considered to be a barometer of the delta's health -- be placed on the state's list of endangered species. The smelt's numbers have plummeted in recent years, a decline blamed on water shipments to Southern California, invasive species and poor water quality.

In recent decades, the delta has come under increasing economic and environmental stresses. The hundreds of miles of levees that protect the region's croplands and the huge pumps near Tracy are frail and weakening.

Compounding stress on the levees is soil subsidence. More than a century of intensive farming has caused the delta's peat-based soils to compact and oxidize. In many areas, fields have sunk 20 feet below sea level.

Finally, the delta is teetering on environmental collapse. Native species like the smelt have dwindled drastically. Nonnative freshwater plants and animals have invaded the ecosystem. Polluted agricultural drainage seeps into the waterways.

In general, governmental attempts to deal with the delta -- most recently through the auspices of CalFed, a joint state and federal agency created to solve California's water woes -- have failed.

"We're really at a multi-faceted crisis point," said Ellen Hanak, an institute fellow who produced the report with experts from UC Davis. "The levees are only getting worse, and we have acute problems in the ecosystem. People are really questioning business as usual."

The institute suggests five alternative ways to fix the delta, a 1,250-square-mile expanse of farmland, sloughs and marshes connected to San Francisco Bay. The report rejected options of leaving the delta as it is, abandoning the region entirely and armoring the levees protecting several large agricultural tracts.

Cost estimates for the five alternatives still under consideration vary from $700 million to "several billion," and annual costs would range from less than $30 million to $100 million.

All of the suggestions in the report involve shifting the western delta from a freshwater system to a variable one. This makes particular sense from an ecological perspective, Hanak said, because the delta's native species evolved with fluctuating cycles of fresh and salt water.

Tina Swanson, a senior scientist with the Bay Institute, a Novato advocacy group that promotes preservation of San Francisco Bay and the delta, said the study properly identifies the lack of salinity fluctuations in the system as a key problem.

"The reason we have such a terrible problem with invasive species in the delta is because virtually all of them are keyed to freshwater -- they can't tolerate salt. Restoring variability is one of the best things we can do," Swanson said.

Two of the alternatives recommended by the report are relatively low-tech. One, the "Eco-Delta" option, generally would manage the region as a kind of reserve for key native species; the "Opportunistic Delta" plan would limit water exports except during times of high flow on the Sacramento River.

Two other plans would involve the construction of a peripheral canal around the delta to deliver water to the big Tracy pumps. A fifth alternative would create a waterway through the delta that would accomplish much the same effect.

Delta farmers and fisheries advocates generally have opposed the idea of a peripheral canal because it could make it easier to shunt more freshwater away from the delta.

"It's an extension of the same old water grab," said Dante John Nomellini, the manager and attorney for the Central Delta Water Agency, a district that supplies water to farmers and residential tracts on 120,000 acres of land in western San Joaquin County. "Whenever anyone starts talking about connecting the Sacramento River to the pumps, it's really about exporting more water south."

Bill Kier, a consultant who has worked on delta and Klamath River fisheries issues since 1957, also is wary of a peripheral canal or anything that resembles it.

"What we have to remember is that a significant amount of freshwater will still be needed for any system that can sustain native fish," Kier said.

Jeffrey Mount, a co-author of the study and a professor of geology at UC Davis, said the study's alternatives address the delta as it is, not as it was.

"The delta (of the 19th century) is gone," Mount said. "It's not coming back. We have a new designer delta, and it is legitimate to ask the question if we have been better off with a static, homogenous freshwater system rather than a (variable) one. Clearly, we haven't."

Mount said that a complex of forces beyond human control -- rising sea levels, earthquakes, continued soil compaction, changes in Sierra precipitation that might increase the intensity of runoff episodes -- ultimately could cause the levees to collapse, abruptly changing the delta regardless of policy or planning.

Changes made now could avoid or limit potentially catastrophic problems with the delta, Mount said. And there could be a collateral benefit, he said: greater flexibility in how water is delivered around the state.

Greg Gartrell, the assistant general manager for the Contra Costa Water District, an agency that gets its drinking water from the delta, said a hybrid solution could emerge.

But he cautioned that the salty delta suggested by the report could make its water unusable for both his district and local farmers.

The report's real value, say some analysts, is that it's the first serious attempt in many years to break the delta policy logjam.

"There are several things here that we haven't seen fully addressed before," said Barry Nelson, a senior policy analyst for the Natural Resources Defense Council, an environmental group. "Not just managing water differently, but the impacts of climate change and urbanization. Ultimately, it suggests we have put too much reliance on the delta to meet our water needs, and that we have to look elsewhere."